John Fickle,
You want everything to be set up "perfect". What you should have learned by now is there is no definition of "perfect" in audio. There is what somebody else think sounds best, there is what you think sounds best and there is what measures most accurately compared to the input.
You can, (and do), find fault with each of these, going back and forth between what sounds best and what measures best. YPAO sets your sub distance for phase mgmt. If you think it sounds better with them set closer, set them closer. If you want a line item buried deep within your AVR setup menus to match a tape measure, set them to match. If you want to take advantage of precision phase matching, leave them alone.
In other words, you must decide which "perfect" you want before asking the question. If you want measurement perfect, we can help. If you want what sounds best to you perfect, experiment.